Bioinformatics Links Directory : Sequence Retrieval and Submission

This section contains links for sequence retrieval and submission. The resources include alignment, sequence analysis as well as visualization tools.

AliasServer - (Found July 2, 2008 )

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.
http://cbi.labri.fr/outils/alias/

Swiss-Shop - (Found July 2, 2008 )

Submit sequence, pattern or keywords to receive email alert when new sequences of interest appear in SwissProt.
http://us.expasy.org/swiss-shop/

Sequin - (Found July 2, 2008 )

Desktop tool developed by the NCBI for editing, annotating and submitting DNA sequences to any of the three DNA sequence submission sites (DDBJ, EMBL or GenBank).
http://www.ncbi.nlm.nih.gov/Sequin/index.html

SeqHound - (Found July 2, 2008 )

Seqhound is a sequence retrieval system that provides access to biological sequence, structure and functional annotation data. Seqhound can be accessed via the web interface, through the remote API, or by installing locally.
http://seqhound.blueprint.org/

SAKURA - (Found July 2, 2008 )

SAKURA is the DDBJ DNA Database Submission System.
http://sakura.ddbj.nig.ac.jp/

PubCrawler - (Found July 2, 2008 )

It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).
http://pubcrawler.gen.tcd.ie/

PAZAR - (Found July 2, 2008 )

PAZAR is an open access and open source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools designed to submit and query data related to the regulation of gene expression.
http://www.pazar.info/

NCBI Influenza Virus Sequence Annotation Tool - (Found July 2, 2008 )

The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.
http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi

NCBI Human DNA Reference Sequence - (Found July 2, 2008 )

Downloadable human DNA reference sequence. Annotation of genes and other genomic features will be available for browsing when complete.
http://www.ncbi.nlm.nih.gov/genome/seq/

MRS - (Found July 2, 2008 )

MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.
http://mrs.cmbi.ru.nl/